title: Transcriptomic analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring after early-life exposure to permethrin 10 microg/L

city: Palavas

first: Mélanie

last: Blanc

address: Route de Maguelone

department: UMR MARBEC

institute: INRAE

summary: In the present study, zebrafish were exposed to permethrin during early-life, and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at adulthood, whereas males from the F1 and F2 generations showed a decrease in anxiety-like behavior. Thus, we performed transcriptomic changes to identify underlying molecular mechanisms. They showed limited overlap between sex and generations. In F0, genes and pathways related to glutamatergic synapse activity (Gene Ontology and Reactome databases) were significantly enriched and may explain the behavioral effects. In F1 and F2 generations, mechanisms are less clear as limited changes which could correlate with behavior were observed in the F1 generation.

overall_design: RNA-sequencing was performed on males and females from the F0, F1 and F2 generations (4 replicates treatment, 4 replicates control for each sex and each generation)

first: Steffen

last: Keiter


title: Epigenomic (RRBS) analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring after early-life exposure to permethrin 10 microg/L

status: Public on Jul 01 2021

country: France

type: Methylation profiling by high throughput sequencing

summary: In the present study, zebrafish were exposed to permethrin during early-life, and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at adulthood, whereas males from the F1 and F2 generations showed a decrease in anxiety-like behavior. We performed transcriptomic analyses on whole brains (GSE154020), and here, we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing, we had to perform a correction on the raw data (CombaT) in order to remove a batch effect (flow-cell). We made sure that this did not create any false-positive differentially methylated region. Processed files available are the results from methyl calling before batch correction(with a min coverage >= 5 per C). A matrix of corrected data is available as supplementary file.

overall_design: Reduced-representative bisulfite sequencing was performed on males and females from the F0, F1 and F2 generations (4 replicates treatment, 4 replicates control for each sex and each generation. Except only 3 treated male F0)


title: TDP-43, an ALS/FTD causal gene, regulates SREBF2-mediated cholesterol metabolism in the CNS

city: Singapore

first: Shuo-Chien

last: Ling

state: Singapore

address: 12 Science Drive 2, MD1, 16-03-H

department: Physiology

country: Singapore

institute: National University of Singapore

type: Expression profiling by high throughput sequencing

summary: Maintaining cholesterol homeostasis is essential for health of all animal cells. Because of blood-brain barrier, de novo cholesetrol biosynthesis and intercellular cholesterol transport is thought to maintain cholesterol homeostasis within the central nervous system (CNS). Here, we showed that TDP-43, the pathological signature protein for amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), regulates SREBF2-mediated cholesterol metabolism in the central nervous system (CNS). Unbiased transcriptomic analysis of mice with oligodendroglial TDP-43 deletion revealed a progressive and pathway-wide disruption in the cholesterol metabolism correlating with reduced myelination and cholesterol level. Molecularly, TDP-43 binds directly to mRNA of SREBF2, the master transcription regulator for cholesterol metabolism, and multiple mRNAs encoding proteins in the cholesterol biosynthesis and uptake, including HMGCR, HMGCS1, and LDLR. Depletion of TDP-43 leads to reduced SREBF2 and cholesterol level in vitro and in vivo. The cholesterol reduction can be rescued by reintroducing either the nuclear portion of SREBF2 or LDLR, the latter of which is the receptor for cholesterol-containing low-density lipoproteins (LDLs). Furthermore, LDLR are observed to co-aggregate with pathological TDP-43 in oligodendrocytes of FTD patients and motor neurons of sporadic ALS patients. Taken together, our data indicates that TDP-43 is required to maintain SREBF2-dependent cholesterol homeostasis in the CNS, and disturbance of cholesterol metabolism may be involved in ALS, FTD and TDP-43 proteinopathies-related disease.

overall_design: Differential gene expression analysis in spinal cord sections of mice with TDP-43 deletion in mature oligodendrocytes at P21 and P60 days

first: Jer

middle: C

last: Chang

first: Kenneth

last: Lim

first: Yun

middle: H

last: Wan

first: Olubankole

middle: A

last: Arogundade

first: Aivi

middle: T

last: Nguyen

first: Maria

middle: J

last: Rodriguez

first: Amaury

last: Gassiot

first: Juat

last: Foo

first: Shawn

last: Hoon

first: Su

middle: M

first: Seung

last: Kim

first: Markus

middle: R

last: Wenk

first: Edward

middle: B

last: Lee

first: John

last: Ravits

first: Greg

last: Tucker-Kellogg

first: Shuo


title: Zebrafish sex differentiation under LPS-mediated inflamatory process.

city: Barcelona

first: Laia

last: Ribas

address: Passeig Maritim 37-49

country: Spain

institute: Institut de Ciencies del Mar

summary: Here the LPS effects on sex differentiation were studied. Dose-response, survival, gene expression methylation levels and sex ratios were recorded

overall_design: zebrafish larva were treated with LPS for P. aeruginosa. Methylation Bisulfite sequencing was performed as described in Anastasiadi el al., 2018

first: J

last: Moraleda

first: M

last: Caballero-Huertas

first: N

last: Roher

first: L


title: Sexual dimorphic methylation patterns in IL1b and Casp9 in the zebrafish gonads

overall_design: Ovaries and testes

first: S

last: Joly


title: The transcriptional repressor REST is a major suppressor of endocrine differentiation during pancreas organogenesis.

status: Public on Jun 30 2021

first: Loris

last: Mularoni

address: Gran Via de l’Hospitalet, 199

department: P-CMR[C]

institute: IDIBELL

type: Genome binding/occupancy profiling by high throughput sequencing

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: The transcriptional repressor REST is a major suppressor of endocrine differentiation during pancreas organogenesis [RNA-seq]

summary: Purpose: Decipher the role of REST in pancreas organogenesis and endocrine differentiation (REST RNAseq-samples E18.5 pancreas)

overall_design: Identification of differential expressed genes between WT and REST KO E18.5 pancreatic samples

first: Goutham

last: Atla

first: Meritxell

last: Rovira

first: Jorge

last: Ferrer


title: The transcriptional repressor REST is a major suppressor of endocrine differentiation during pancreas organogenesis [ChIP-seq]

summary: Purpose: Decipher the role of REST in pancreas organogenesis and endocrine differentiation (REST ChIPseq-samples E13.5 and E18.5 pancreas)

overall_design: 2 biological replicates of E13.5 (4-6 pancreas per sample) and 3 biological replicates E18.5 pancreas (3-4 pancreas per sample)


title: Probing tumorigenic potentials of the genetic interactions reconstituted in murine fallopian tube organoids

city: Chiba

first: Yoshitaka

last: Hippo

state: Chiba

address: 666-2 Nitona-cho, Chuo-ku

country: Japan

institute: Chiba Cancer Center

summary: Despite histological diversity in the subcutaneous nodules and tumors, the derived tumor-derived organoids stereotypically exhibited cystic featuresTo clarify molecular differences among the p53-null falopian tube-derived tumors driven by KrasG12D, Pik3caH1047R, and Apc580D, the transcriptome across tumor-derived organoidss, originating organoids before inoculation, p53-null organoids without driver mutations, and organoids without recombination as a reference were compared.

overall_design: The Trp53flox/flox mice-derived FT organoids transduced with the control vector pLKO.1 served as a reference for gene expression. Three pairs of organoids before injection and derived from tumors were analyzed.

first: Yoshiaki

last: Maru


title: Kras activation in endometrial organoids drives cellular transformation and epithelial-mesenchymal transition

summary: We found that in KrasG12D-expressing endometrial organoids, Pten knockdown did not confer tumorigenicity, but Cdkn2a knockdown or Trp53 deletion led to the development of carcinosarcoma (CS), a rare, aggressive tumor comprising both carcinoma and sarcoma.To better characterize the pathogenesis of CS from organoids, we conducted a transcriptome analysis.

overall_design: A total of 8 samples. For KrasG12D organoids with both Cdkn2a knockdown (#4) and Trp53 deletion (#5, #6), the pre-inoculated organoids and tumor-deribved organoids were analyzed. KrasG12D organoids with shLuc were also analyzed. Endometrial organoids without lentiviral infection served as reference.


title: CD249+ fibroblasts vs CD249 neg fibroblasts

city: West Hollywood

first: AGCT

last: Core

state: CA

address: 8687 Melrose Ave, PDC B230

department: BMS

country: USA

institute: Cedars Sinai Medical Center

summary: Bulk sequencing of murine lung fibroblasts expressing a potential novel marker of lipofibroblasts (Enpep aka. Cd249).

overall_design: Murine lungs were digested using conventional methods and a single cell suspension generated. Fibroblasts (CD45/CD326/CD31 negative) expressing Cd249 were flow sorted and collected. A equal number of CD249 negative fibroblasts from the same lung were collected at the same time. Total RNA was isolated using the Qiagen RNeasy Micro kit and stored at -80C until analyzed. All samples were submitted together submitted to the CSMC Genomics Core facilty for bulk RNA sequencing.

first: Simon

last: Rowan

first: Xue

last: Liu

first: Dianhua

last: Jiang


title: An Atlas of Gene Regulatory Elements in Adult Mouse Cerebrum

city: La Jolla

first: Yang

last: Li

address: 9500 Gilman Dr

institute: University of California San Diego

summary: The mammalian cerebrum performs high-level sensory, motor control and cognitive functions through highly specialized cortical networks and subcortical nuclei. Recent surveys of mouse and human brains with single cell transcriptomics and high-throughput imaging technologies have uncovered hundreds of neuronal cell types and a variety of non-neuronal cell types distributed in different brain regions, but the cell-type-specific transcriptional regulatory programs responsible for the unique identity and function of each brain cell type have yet to be elucidated. Here, we probe the accessible chromatin in >800,000 individual nuclei from 45 regions spanning the adult mouse isocortex, olfactory bulb, hippocampus, and cerebral nuclei, and use the resulting data to map the state of 491,818 candidate cis regulatory DNA elements (cCREs) in 160 distinct sub-types. We find high specificity of spatial distribution for not only excitatory neurons, but also most classes of inhibitory neurons and a subset of glial cell types. We characterize the gene regulatory sequences within these cell types that underlie their regional specificity. We further link a significant fraction of the cCREs to putative target genes expressed in diverse cerebral cell types and uncover transcriptional regulators involved in a broad spectrum of molecular and cellular pathways in different neuronal and glial cell populations. Our results provide a foundation for comprehensive analysis of gene regulatory programs of the mammalian brain and assist in the interpretation of non-coding risk variants associated with various neurological diseases and traits in humans. To facilitate the dissemination of information, we have set up a web portal (http://catlas.org/mousebrain).

overall_design: Additional single nuclei ATAC-seq with two replicates.

middle: E

first: Sebastian

last: Preissl

first: Bing

last: Ren


title: SFPQ promotes an oncogenic transcriptomic state in melanoma

city: Leeds

first: Adrian

last: Whitehouse

address: Leeds

department: 1School of Molecular and Cellular Biology

country: United Kingdom

institute: University of Leeds

summary: Analysis of SFPQ interactome  in primary melanocytes  and melanoma cells. Results provide insight into the oncogenic reprogamming of SFPQ-RNA interactome and  especially the interactions with key melanoma-associated coding transcripts.

overall_design: RNA-IP with SFPQ antibody followed by RNA sequencing in primary melanocytes  and melanoma cells.

first: James

last: Boyne

first: Chinedu

last: Anene


title: Transcriptome-based prediction of nitrogen use efficiency in Arabidopsis and maize - I

city: New York

first: Chia-Yi

last: Cheng

state: NY

address: 12 Waverly Place

department: Biology

institute: New York University

summary:
Inferring phenotypic outcome from genomics features is the promise and challenge for basic and applied research. Functionally testing whether the feature(s) with predictive power can shed light on the underlying mechanism remains largely unexplored. We address these gaps by applying a machine learning approach to predict phenotypes based on transcriptome data. We validate the predictive models in silico using out-of-sample varieties and in planta by reverse genetics. Our study primarily focuses on a agronomic trait nitrogen use efficiency (NUE), but the described approach can be applied to any phenotype across biology, agriculture and medicine.
We measure NUE and gene expression from natural and cultivated varieties of Arabidopsis and maize, respectively, under low and high N environments. We integrate transcriptomics across a model and a crop and demonstrate that identifying the evolutionarily conserved N-responsive differentially expressed genes is an efficient technique to reduce the feature dimensionality, which ultimately improves the predictive power of the gene-to-trait models learned. Furthermore, including a model organism with a comprehensive mutant collection has enabled the efficient validation of the role candidate genes with predictive power in NUE outcomes.
Using the matched transcriptomic and phenotypic data from a model and crop species, we present an analysis pipeline to infer a complex trait from transcript abundance. This analysis pipeline can be applied to any other organisms to uncover novel genes underpinning physiological traits of interest.

sample_organism:
Arabidopsis thaliana
Zea mays

platform_organism:
Arabidopsis thaliana
Zea mays

overall_design:
Arabidopsis: 108 samples were analyzed, including 18 accessions in two nitrogen conditions with 3 replicates each.
Maize: 91 samples were analyzed, including 16 genotypes in two nitrogen conditions.

first: Chia

middle: Y

first: Gloria

last: Coruzzi

first: Stephen

middle: P

last: Moose


title: The CTCF/LncRNA-PACERR/EP300 complex in TAMs promotes the malignant progression of pancreatic ductal adenocarcinoma (PDAC) by docking at the PTGS2 promoter region

city: Shanghai

first: Xuelong

last: Wang

address: No. 100 Banxia Road

country: China

institute: Chinese Academy of Sciences

summary: The unregulated expression of COX-2 in tams is causally related to the occurrence, development and outcome of pancreatic ductal adenocarcinoma. We describe a new basic level of transcriptional control of COX-2 expression. Constructing in vivo and in vitro TAM model lines, we found that CTCF plays a significant role in the chromatin remodeling of pancreatic cancer-related macrophages, and showed that CTCF, which acts as both a transcription factor and an insulator, establishes an open chromatin domain, and Induced the expression of LncRNA PACERR in the upstream promoter region of PTGS2. The newly transcribed LncRNA PACERR binds to the RNA binding region of CTCF to play a cis-regulatory role. The formation of CTCF/LncRNA PACERR complex contributes to the recruitment of EP300 histone acetylation transfer, which increases the global scope of histone acetylation and induces the expression of PTGS2. Our findings reveal that CTCF and LncRNA that was regulated by CTCF at the same position work together to form a complex of CTCF/LncRNA PACERR/EP300 and dock in the PTGS2 promoter region to mediate the unexpected mechanism of PTGS2 expression. And LncRNA PACERR as a new potential target for regulating the malignant progression of pancreatic cancer.

overall_design: Examination of different histone modifications, chromatin accessibility and gene expression in in vivo and in vitro TAM  model lines.

first: Yihao


title: Analysis of miRNA expression patterns in tetracycline (Tet) inducible Scl/tTA-BCR/ABL (Scl-BA) transgenic mouse hematopoietic stem-progenitor cells.

first: Zhiwei

last: Chen

address: Room 807, Research and Education Plaza, 197 Ruijin 2nd Road, Luwan District, Shanghai, PRC

department: Shanghai Institute Of Hematology

institute: Shanghai Jiao Tong Universtiy School of Medicine

summary: To further define the roles of miRNAs in the pathogenesis of CML, we have employed miRNA microarray expression profiling as a discovery platform to identify miRNAs with the potential to drive or accelerate CML progression. Hematopoietic stem-progenitor cells miRNA profiles of BA mice after BCR/ABL expression induced for 0 week and 3 weeks were generated by miRNA microarray. Expression of six miRNAs (miR-126a-3p, miR-130a-3p,miR-142a-5p, miR-142a-3p, miR-29c-3p and miR-30c-5p) from this signature was quantified in the same RNA samples by real-time PCR, confirming low variability in BCR/ABL expressing cells.

overall_design: Hematopoietic stem-progenitor cells (lin-c-kit+sca1+, LSK) of BA mice after BCR/ABL expression induced for 0 week and 3 weeks were sorted by FACS, LSK cells from three mice were mixed in each group.

first: Qiuhua

last: Huang


title: VcdRP target identification

city: Jena

first: Kavyaa

last: Venkat

address: Winzerlaer Straße 2

country: Germany

institute: Friedrich-Schiller-University Jena

summary: In this study we determined the target spectrum of the Vibrio cholerae dual RNA regulator VcdRP via pulse-expression of different variants followed by RNA-sequencing.

overall_design: V. cholerae ΔvcdRP cells carrying inducible pBAD expression vectors were grown to early exponential phase (OD600=0.1). Expression was induced by L-arabinose and total RNA samples were collected 15 minutes after induction. The experiment was performed with three independent biological replicates. The following vectors were used: pBAD1K-Ctrl (empty control plasmid), pBAD1K-VcdRP (with the full VcdRP sequence), pBAD1K-VcdR (with a stop codon at the third position of the VcdP peptide) or pBAD1K-VcdP (with a modified nucleotide sequence coding for the VcdP peptide alone).

first: Mona

last: Hoyos

first: Kai

last: Papenfort


title: Chemotherapy-induced transposable elements activate MDA5 to enhance haematopoietic regeneration

status: Public on Jun 28 2021

city: Freiburg

first: Sagar

address: Hugstetter Straße 55

department: Department of Internal Medicine II

institute: University Medical Center Freiburg

summary: Haematopoietic stem cells (HSCs) are normally quiescent, but have evolved mechanisms to respond to stress. Here, we evaluate haematopoietic regeneration induced by chemotherapy. We detect robust chromatin reorganization followed by increased transcription of transposable elements (TEs) during early recovery. TE transcripts bind to and activate the innate immune receptor melanoma differentiation-associated protein 5 (MDA5) that generates an inflammatory response that is necessary for HSCs to exit quiescence. HSCs that lack MDA5 exhibit an impaired inflammatory response after chemotherapy and retain their quiescence, with consequent better long-term repopulation capacity. We show that the overexpression of ERV and LINE superfamily TE copies in wild-type HSCs, but not in Mda5−/− HSCs, results in their cycling. By contrast, after knockdown of LINE1 family copies, HSCs retain their quiescence. Our results show that TE transcripts act as ligands that activate MDA5 during haematopoietic regeneration, thereby enabling HSCs to mount an inflammatory response necessary for their exit from quiescence.

overall_design: Single-cell RNA sequencing was performed on HSCs from Mda5+/+ (IFIH1WT) and Mda5-/- (IFIH1KO) mice.

first: Thomas

last: Clapes

first: Aikaterini

last: Polyzou

last: Sagar

first: Dominic

last: Gruen

first: Eirini

last: Trompouki


title: Transcriptomic characterization of CXCR4C1013G and Eµ-TCL1;CXCR4C1013G CD19+ B cells

status: Public on Jun 27 2021

city: Berlin

first: Matthias

last: Wirth

address: Hindenburgdamm 30

institute: Charité Berlin

summary: Aberrant CXCR4 activity has been implicated in lymphoma pathogenesis, disease progression and resistance to therapies. Using a mouse model with a gain-of-function CXCR4 mutation (CXCR4C1013G) that hyperactivates CXCR4 signaling, we identified CXCR4 as a crucial activator of multiple key oncogenic pathways. CXCR4 hyperactivation furthermore resulted in an expansion of transitional B1 lymphocytes, which represent the precursors of chronic lymphocytic leukemia (CLL). Indeed, CXCR4 hyperactivation led to a significant acceleration of disease onset and a more aggressive phenotype in the murine Eµ-TCL1 CLL model. Hyperactivated CXCR4 signaling cooperated with TCL1 to cause a distinct oncogenic transcriptional program in B cells, characterized by PLK1/FOXM1-associated pathways. In accordance, Eµ-TCL1;CXCR4C1013G B cells enriched a transcriptional signature from patients with Richter’s syndrome, an aggressive transformation of CLL. In summary, we here identify CXCR4 hyperactivation as a co-driver of an aggressive lymphoma phenotype. Here we make available the transcriptomic data of CD19+ B cells from bone marrow and spleen of 6-week-old WT, CXCR4C1013G, Eµ-TCL1 and Eµ-TCL1;CXCR4C1013G mice.

overall_design: 4 genotypes: WT, CXCR4C1013G, Eµ-TCL1, Eµ-TCL1;CXCR4C1013G;    2 tissues: CD19+ B cells from spleen, CD19+ B cells from bone marrow;    5 replicates per biological group;     40 samples in total

first: Richard

last: Lewis

first: H

last: Maurer

first: Nikita

last: Singh

first: Irene

last: Gonzalez-Menendez

first: Markus

last: Schick

first: Le

last: Zhang

first: Konstandina

last: Isaakidis

first: Anna

middle: K

last: Scherger

first: Veronika

last: Schulze

first: Junyan

last: Lu

first: Thorsten

last: Zenz

first: Katja

last: Steiger

first: Roland

last: Rad

first: Leticia

last: Quintanilla-Martinez

first: Marion

last: Espeli

first: Karl

last: Balabanian

first: Ulrich

last: Keller

first: Stefan

last: Habringer


title: FFPE-ATAC decodes the chromatin accessibility from the clinical archived FFPE tissues

city: Uppsala

first: xingqi

last: chen

address: Uppsala Biomedical Center C10:2, Husargatan 3

department: IGP

country: Sweden

institute: Uppsala University

summary: We present FFPE-ATAC, a new ATAC-seq tool for chromatin accessibility profiling that decodes the chromatin accessibility from mouse FFPE tissue and clinical archived FFPE tissues. The FFPE-ATAC generates the high-quality chromatin accessibility profiles from clinical FFPE tissue sections with 5-20 µm thickness, and reveals the disease-associated regulatory elements in different types of FFPE archived tissue. FFPE-ATAC enables to decode the chromatin states regulating the gene regulation in the cancer and understand the epigenetic regulation in the translational studies.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: FFPE-ATAC of mouse liver,cerebellum, and human colonrectal cancer samples. Omni-ATAC of mouse liver sample.

first: Xingqi

last: Chen

first: Hua

first: Vamsi

last: Polavarapu

first: Xingwei

last: Peng


title: Expression data from malaria-specific mouse CD4 T cell (PbT-II) subset after Plasmodium chabaudi infection

status: Public on Jun 23 2021

city: Nagasaki

first: Katsuyuki

last: Yui

state: Nagasaki

address: 7F, 1-12-4, Sakamoto

institute: Nagasaki University

summary: Upon activation, specific CD4+ T cells up-regulate the expression of CD11a and CD49d, surrogate markers of pathogen-specific CD4+ T cells. However, using T-cell receptor transgenic mice specific for a Plasmodium antigen, termed PbT-II, we found that activated CD4+ T cells develop not only to CD11ahiCD49dhi cells, but also to CD11ahiCD49dlo cells during acute Plasmodium infection. CD49dhi PbT-II cells, localized in the red pulp of spleens, expressed transcription factor T-bet and produced IFN-γ, indicating that they were type 1 helper T (Th1)-type cells. In contrast, CD49dlo PbT-II cells resided in the white pulp/marginal zones and were a heterogeneous population, with approximately half of them expressing CXCR5 and a third expressing Bcl-6, a master regulator of follicular helper T (Tfh) cells. In adoptive transfer experiments, both CD49dhi and CD49dlo PbT-II cells differentiated into CD49dhi Th1-type cells after stimulation with antigen-pulsed dendritic cells, while CD49dhi and CD49dlo phenotypes were generally maintained in mice infected with Plasmodium chabaudi. These results suggest that CD49d is expressed on Th1-type Plasmodium-specific CD4+ T cells, which are localized in the red pulp of the spleen, and can be used as a marker of antigen-specific Th1 CD4+ T cells, rather than that of all pathogen-specific CD4+ T cells.

overall_design: PbT-II cells were adopted transferred into B6 mice and infected with Plasmodium chabaudi. Seven days after infection, we sorted subsets of PbT-II cells based on their expression of CD11a and CD49d expression.

first: Jiun-Yu

last: Jian

first: Shin-Ichi

last: Inoue

first: Ganchimeg

last: Bayarsaikhan

first: Mana

last: Miyakoda

first: Daisuke

last: Kimura

first: Kazumi

first: Eriko

last: Nozaki

first: Takuya

last: Sakurai

first: Daniel

last: Fernandez-Ruiz

first: William

last: Heath


title: POLYseq: A poly(ß-amino ester)-based vector for multifunctional cellular barcoding

status: Public on Jun 22 2021

city: Cincinnati

first: Andrew

last: Dunn

state: Ohio

address: 3333 Burnet Ave R3.543

department: Gastroenterology

institute: Cincinnati Children's Hospital Medical Center

summary: Despite evolving stem cell and organoid application of next-generation sequencing (NGS) at single cell level, current techniques in NGS library preparation are restrictive as individual samples within a single library are indistinguishable, necessitating the laborious and costly preparation of distinct libraries for each sample. To combat this challenge, we report the development of a novel poly(ß-amino) ester labeling system synthesized with inexpensive, common reagents, termed POLYseq, capable of efficiently delivering fluorescent molecules or sample-distinguishing DNA barcodes through non-covalent binding enabling rapid creation of custom libraries.

overall_design: Delivery of Next-Gen readable ssDNA barcodes by POLYseq into individual human liver organoid samples and pooled cell lines

first: Yuqi

last: Cai

first: Takanori

last: Takebe


title: Investigation of therapeutic response markers for acupuncture in Parkinson's disease: An exploratory pilot study

status: Public on Jun 19 2021

city: Daejeon

first: Sang-Min

last: Park

address: Youseong-Daero

department: College of Pharmacy

country: South Korea

institute: Chungnam National University

summary:
Introduction: In our previous study, we demonstrated that acupuncture improved gait disturbances, such as hypometric gait, in patients with Parkinson’s disease (PD). To investigate specific genes that indicate a therapeutic response to acupuncture, we analyzed transcriptome alterations following acupuncture using blood samples collected in our previous clinical trial.
Methods: We reanalyzed the clinical data of patients and selected a representative patient with PD for transcriptomic analysis following acupuncture. We examined the expression changes of PD biomarker genes known to be consistently dysregulated in both the brain and blood in patients with PD. We validated these gene expression changes using quantitative real-time polymerase chain reaction (qPCR) in the blood of five other patients with PD who received acupuncture treatment.
Results: After acupuncture treatment, the transcriptomic alterations in the representative patient were similar to those induced by dopaminergic therapy. Among PD biomarkers, ankyrin repeat domain 22 (ANKRD22), which is upregulated after dopaminergic therapy, and synapsin 1 (SYN1), which is the common gene to indicate synaptic dysfunction in PD, were upregulated following acupuncture. These alterations correlated with changes of gait parameters in patients with PD.alterations following acupuncture using blood samples collected in our previous clinical trial.
Conclusion: This is the first report on gene expression changes and improvement of gait disturbance in patients with PD following acupuncture. Our data suggest that ANKRD22 and SYN1 can be used as biomarkers for therapeutic response to acupuncture in patients with PD, especially those with gait disturbance.alterations following acupuncture using blood samples collected in our previous clinical trial.

overall_design: We performed RNA sequencing analysis of the representative patient with PD of the greatest therapeutic effect on gait after acupuncture (5 and 8 sessions).

first: Gunhyuk

first: Sangsoo

first: Horyong

last: Yoo

first: Jung-Hee

last: Jang


title: Transplantation of patient-specific bile duct bioengineered with chemically reprogrammed and microtopographically differentiated cells

status: Public on Jun 18 2021

city: Rockville

first: Daekwan

last: Seo

state: MARYLAND

address: 1330 Piccard Dr., Ste 103

department: Bioinformatics

institute: Psomagen Inc

summary: Cholangiopathy is a diverse spectrum of chronic progressive bile duct disorders with limited treatment options and dismal outcome. Scaffold- and stem cell-based tissue engineering technologies hold great promise for the reconstructive surgery and tissue repair. Here, we report a combined application of 3D scaffold fabrication and direct reprogramming of the patient-specific human hepatocytes to a population of pluripotent stem cells to fabricate implantable artificial tissues that imitate mechanical and biological properties of the native bile ducts. The chemically derived hepatic progenitor cells (hCdHs) were generated using two small molecules A8301 and CHIR99021 and seeded inside the tubular scaffold engineered as synergistic combination of two layers. The inner electrospun fibrous layer was made of nanoscale-macroscale polycaprolactone fibers acting to promote the hCdHs attachment, alignment, and differentiation, while the outer microporous acellular foam layer served to increase mechanical stability. The two layers of fiber and foam were fused robustly together thus creating a coordinated mechanical flexibility to exclude any possible breaking or tear during surgery. The gene expression profiling and histochemical assessment confirmed that hCdHs acquired the biliary epithelial phenotype and filled the entire volume surface of fibrous matrix after two weeks of growth in cholangiocyte differentiation medium in vitro. The fabricated construct replaced the macroscopic part of the common bile duct (CBD) and re-stored the bile flow in a rabbit model of acute CBD injury. Animals which received the acellular scaffolds did not survive the replacement surgery. Thus, the artificial bile duct constructs populated with the patient-specific hepatic progenitor cells could provide a scalable and compatible platform for treating bile duct diseases.

overall_design: Transcriptome analysis for chloangiocytes differentiation of human chemically induced hepatic stem cells (hCdHs)

first: Jaemin

last: Jeong

first: Dongho

last: Choi


title: The impact of influenza pulmonary infection and inflammation on vagal bronchopulmonary sensory neurons

status: Public on Jun 20 2021

city: Parkville

first: Matthew

last: Ritchie

state: Victoria

address: 1G Royal Parade

department: Epigenetics and Development Division

country: Australia

institute: The Walter and Eliza Hall Institute of Medical Research

summary: Influenza A virus (IAV) is rapidly detected in the airways by the immune system, with resident parenchymal cells and leukocytes orchestrating viral sensing and the induction of antiviral inflammatory responses.  The airways are innervated by heterogenous populations of vagal sensory neurons which also play an important role in pulmonary defense.  How these neurons respond to IAV respiratory infection remains unclear.  Here, we use a murine model to provide the first evidence that vagal sensory neurons undergo significant transcriptional changes following a respiratory IAV infection.  RNA sequencing on vagal sensory ganglia showed that IAV infection induced the expression of many genes associated with an antiviral and pro-inflammatory response

overall_design: Transcriptome of vagal sensory ganglia obtained from mice infected with a respiratory pathogen (influenza A)

first: Charity

middle: W

last: Law

first: Albert

last: Zhang

first: Alice

last: McGovern


title: Histone demethylase SlJMJ7 Integrates DNA demethylation, ethylene signal and major ripening-related transcription factors in coordination of fruit ripening in tomato

city: guangzhou city

first: Ding

last: xiaochun

state: guangdong

address: 723 xingke road, tianhe district

institute: SOUTH CHINA BOTANICAL GARDEN

summary: Combinational analyses of genome-wide transcription, binding sites and histone H3K4 trimethylation profiles revealed that SlJMJ7 directly binds and represses the expression of a series of key ripening-associated factors, including ethylene biosynthesis genes ACS2/4/8 and ACO2, DNA demethylase DML2, as well as the ripening-related transcription factors RIN and NOR by removal the mark of H3K4-trimethylation. Moreover, SlJMJ7 directly and indirectly modulates the transcription of genes related to diverse physiological traits of fruit ripening.

overall_design: Tomato DNA methylation profiles of wild type (WT) and transgenic knockout of JMJ7 lines (jmj7) at 38 days after anthesis.

first: Xiaochun

last: Ding

first: Xuncheng

last: Liu

first: Zhiwei

last: Li

first: Guoxiang

last: Jiang

first: Yunbo

last: Song

first: Dandan

first: Jing

last: Zeng

first: Hanzhi

last: Liang

first: Lu

last: Xiao

first: Huiling

last: Yan

first: Hongmei

last: Lai

first: Yueming

first: Xuewu

last: Duan


title: CMV-CTL RNA-seq at the early & late phases

city: Saitama

first: Hideki

last: Nakasone

address: 1-847, Amanuma-cho, Omiya-ku

department: Hematology

institute: Jichi Medical University Saitama Medical Center

summary: We conducted immune- and RNA-sequencing of HLA-A24-restricted CMVpp65-specific CTLs to better understand the immune reconstitution of CMV-CTLs after allo-HCT. To the best of our knowledge, this is the first report on the features of TCRβ-CDR3, diversity, and GEP of HLA-A24 CMV-CTLs according to the CMV-reactivation pattern among recipients after allo-HCT. In addition, we further sought to demonstrate homogeneity or heterogeneity according to individual CTL clones using single-cell RNA-sequencing technology.

overall_design: Compare GEP in CMV-CTLs according to the CMV-reactivation pattern and donor CMV serostatus at the early and late phases after allo-HCT.


title: Tak1-inhibitors are cytotoxic for multiple myeloma cells alone and in combination with melphalan

status: Public on Jun 17 2021

city: Trondheim

first: Kristine

last: Misund

address: Prinsesse Kristinas gate 1

department: Department of Clinical and Molecular Medicine

country: Norway

institute: NTNU

summary: To determine which genes are affected by NG25 and melphalan, we performed an RNA-seq on INA-6 cells treated with NG25, melphalan or a combination of the two. GSEA focusing on the hallmark pathways showed that melphalan-treatment upregulated genes involved in UV-response, DNA-repair, p53-pathway and TNF-signaling via NF-kB. NG25 induced expression of genes involved in cholesterol homeostasis and mTORC1-signaling and down-regulated MYC- and E2F-targets. MYC is a central driver of MM pathology, and regulate survival as well as cell cycle control through E2F. NG25 reversed the melphalan-induced UV-response.

overall_design: Examination of triplicates of four conditions of multiple myeloma INA-6 cells; control, treated with NG25, treated melphalan, or treated woth both NG25 and melphalan for 6 hours

first: Kristian

last: Starheim


title: Spatial immunophenotypes predict response to anti-PD1 treatment and capture distinct paths of T-cell  evasion in triple negative breast cancer

status: Public on Jun 12 2021

city: Rotterdam

first: Dora

last: Hammerl

address: Erasmus MC Cancer Institute, Doctor Molewaterplein 40, BE430 (room)

department: Mediacl Oncology

country: Netherlands

institute: Erasmus MC Cancer Institute

summary: Only a subgroup of triple-negative breast cancer (TNBC) responds to immune checkpoint inhibitors (ICI). To better understand lack of response to ICI, we analyzed 681 TNBCs for spatial immune cell contextures in relation to clinical outcomes as well as pathways of T-cell evasion. Excluded, ignored and inflamed phenotypes were captured by a gene classifier that predicts prognosis of various cancers as well as anti-PD1 response of metastatic TNBC patients in a phase II trial. The excluded phenotype, which was associated with resistance to anti-PD1, demonstrated deposits of collagen-10, enhanced glycolysis, and activation of TGFb/VEGF pathways; the ignored phenotype, also associated with resistance to anti-PD1, showed either high density of CD163+ myeloid cells or activation of WNT/PPARg pathways; whereas the inflamed phenotype, which was associated with response to anti-PD1, revealed necrosis, high density of CLEC9A+ dendritic cells, high TCR clonality independent of neo-antigens, and enhanced expression of T-cell co-inhibitory receptors.

overall_design:
43 TNBC specimen with matched clinical data, IHC data and multiplexed immunofluorescence data were sequenced
****  Submitter declares that the raw data will be deposited in EGA due to patient privacy concerns.  ****

first: Marcel

last: Smid

first: Mieke

last: Timmermans

first: John

last: Martens

first: Reno

last: Debets


title: e18.5 pancreas: WT vs Cyp11a1 KO

status: Public on Jun 25 2021

city: Taipei

first: Meng-Chun

middle: Monica

last: Shih

address: Building G, No. 99, Lane 130, Section 1, Academia Road, Nangang District

country: Taiwan

institute: NLAC

summary: RNA profiling of WT and cyp11a1 KO pancreas at e18.5

overall_design: Two-condition experiment, WT vs. KO pancreas. Biological replicates: 4 control replicates, 4 KO replicates.

first: Monica

first: Bon-chu

last: Chung


title: Sequencing of Argonaute-bound miRNA/mRNA hybrids reveals regulation of the unfolded protein response by microRNA-320a

city: Gainesville

first: Christopher

middle: James

last: Fields

state: Florida

address: 2033 Mowry Road

department: Biochemistry and Molecular Biology

institute: University of Florida

summary: MicroRNAs (miRNA) are short non-coding RNAs widely implicated in development, gene regulation, and disease progression. Most miRNAs utilize the RNase III enzymes Drosha and Dicer for biogenesis in animals. One notable exception is the RNA polymerase II transcription start sites (TSS) miRNAs whose biogenesis requires Dicer but not Drosha. The functional importance of the TSS-miRNA biogenesis pathway has remained uncertain due to their unelucidated targetomes. To better understand the function of TSS-miRNAs, we applied a modified Crosslinking, Ligation, and Sequencing of Hybrids on Argonaute (Ago-qCLASH) to identify the targets for TSS-miRNAs in HCT116 colorectal cancer cells with or without Drosha knockout (KO). We observed that miR-320a hybrids dominate in TSS-miRNA hybrids identified by Ago-qCLASH. Targets for miR-320a are enriched in the eIF2 signaling pathway, a downstream component of the unfolded protein response. Consistently, in miR-320a mimic- and inhibitor- transfected cells, differentially expressed genes are enriched in the eIF2 signaling pathway. Within the Ago-qCLASH data, we identified the endoplasmic reticulum (ER) chaperone Calnexin as a direct miR-320a target, thus connecting miR-320a to the unfolded protein response. During ER stress, but not amino acid deprivation, miR-320a up-regulates ATF4, a critical transcription factor for resolving ER stress. Our study helps to elucidate the targetome of the TSS-miRNAs in colorectal cancer cells and establishes miR-320a as a regulator of unfolded protein response.

overall_design: At least 2 replicates of each Ago antibody (2A8 and 4F9) for each cell type (HCT116 WT, Drosh KO, and Dicer KO) and a total of 4 replicates for each cell type was used in this study.

first: Mingyi

last: Xie


title: Characterisation of the anti-lymphoma activity of pracinostat reveals differential sensitivities of DLBCL cells to HDAC inhibitors

status: Public on Jun 02 2021

city: Bellinzona

first: Luciano

last: Cascione

state: Ticino

address: Via Chiesa 5

department: Lymphoma & Genomics Research Program

country: Switzerland

institute: IOR

summary: 6 lymphoma cell lines (OCILY1, SUDHL4, TOLEDO, WSUDLCL2, PFEIFFER, SUDHL6) have been treated with DMSO, Vorinostat and Pracinostat. The transcriptome has been sequenced after 6hrs and 14 days from the treatment. The gene expression levels have been compared in order to elucidate the differencies and similarities for Vorinostat and Pracinostat compare to DMSO (control group).

overall_design: Transcriptome profiles of 6hrs and 14days for 6 lymphoma cell lines treated with DMSO, Vorinostat and Pracinostat.

first: Francesco

last: Bertoni


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and hnRNPA2B1-KO sw480 cell line Transcriptomes

status: Public on Jun 09 2021

city: Shanghai

first: Jingzhi

last: Tang

state: Shanghai

address: The 15th floor of Building 17,No.160 Pujian Road .

institute: Ren ji Hospital,School of Medicine, Shanghai Jiao Tong University,Shanghai

summary: HNRNPA2B1, an RNA-binding protein, plays a key role in primary microRNA processing, alternative splicing, mRNA metabolism and transport. Interestingly, hnRNPA2B1 also works as an N6-methyladenosine(m6A) reader and is critical during tumorigenesis of various tissue types. However, its role in colon cancer is still unclear. In this study, we aimed to elucidate the biological functions of hnRNPA2B1 and to explore its underlying mechanisms in colon cancer. Methods We examined the expression of hnRNPA2B1 in Oncomine and TCGA databases. Then verified the findings in colon cancer cells and clinical samples with western blotting and immunohistochemistry (IHC). We used CRISPR/Cas9 directed gene editing to knockout hnRNPA2B1 expression in human colon cancer cell line SW480 and carried out both in vivo and in vitro experiments. The results were further confirmed by RNA-seq analysis. We found that hnRNPA2B1 significantly promoted colon cancer cell proliferation both in vitro and in vivo, while knockout of hnRNPA2B1 induced apoptosis and cell cycle arrest in SW480. RNA-seq analysis revealed that the ERK/MAPK pathway was activated by hnRNPA2B1 upregulation. In addition, both hnRNPA2B1 and MAPK pathway were activated in clinical colon cancer specimens and positively correlated. Mechanistically, hnRNPA2B1 appeared to be an upstream regulator of the ERK/MAPK pathway and inhibition of MAPK signaling blocked the effects of hnRNPA2B1. Taken together, our data demonstrated that the RNA-binding protein hnRNPA2B1 promotes cell proliferation and regulates cell cycle and apoptosis of human colon cancer by activating the ERK/MAPK signaling, which may provide a new insight into the development of hnRNPA2B1 as a potential therapeutic target for treatment of colon cancer.

overall_design: RNA sequencing was used to determine the molecular mechanisms of hnRNPA2B1 in human colon cancer cells

first: Zhimin

last: Chen

first: Qi

last: Wang

first: Weijie

last: Hao

first: Weiqiang

last: Gao

first: Huiming

last: Xu


title: Assembly defects of the human tRNA splicing endonuclease contribute to impaired pre-tRNA splicing in pontocerebellar hypoplasia

city: New York

first: Tasos

last: Gogakos

address: 1230 York Ave

institute: The Rockefeller University

type: Non-coding RNA profiling by high throughput sequencing

summary: Our work defines the molecular principles of intron excision in humans and provides evidence that destabilized TSEN contributes to a PCH phenotype by impairing tRNA splicing at the intron-excision step.

overall_design: Ten samples for hydro-tRNAseq from human derived fibroblasts.


title: RNA-Seq and Electrical Penetration Graph Revealed the Role of Grh1-Mediated Activation of Defense Mechanisms towards Green Rice Leafhopper (Nephotettix cincticeps Uhler) Resistance in Rice (Oryza sativa L.)

status: Public on Jun 10 2021

city: Miryang

first: ROLLY

middle: NKULU

last: KABANGE

state: Gyeongsangnamdo

address: Jompiljaero 20, Naei-dong

department: Department of Southern Area Crop Science

institute: Rural Development Administration

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to investigate NGS-derived rice leaf transcriptome profiling (RNA-seq) exposed to green rice leafhopper (GRH) and validated RNA-Seq results using quantitative reverse transcription polymerase chain reaction (qRT–PCR).
Methods: Rice leaf mRNA profiles of 21-day-old wild-type (WT) and Near Isogenic Line (NIL) rice were generated by deep sequencing, in triplicate, using Illumina’s HiSeq™ 4000 Sequencing System. For assembled genes, longest contigs of the assembled contigs were filtered and clustered into the non-redundant transcripts using CD-HIT-EST (Li et al., 2001; Bolger et al., 2014). qRT–PCR validation was performed using ROX and SYBR Green assays.
Results: RNA-Seq results revealed that an average of 1,766,347 (1,240,317 in control and 526,030 GRH treated plants) and 3,676,765 (2,986,748 control and 690,017 GRH) counts per million mapped (CPM) reads were generated from Ilpum and NIL GRH treated plants, respectively. After alignment, more than 75% of all reads were successfully mapped to the reference genome, and 8,859 genes and 15,815,400 transcripts were obtained. GRH infestation caused differential expression of 4265 up-regulated and 4,594 down-regulated genes in Ilpum, while in NIL, 4,479 and 4,380 genes were up- and down-regulated, respectively 48 h post-infestation. A total of 3,424 differentially expressed genes (DEGs, 1,605 up-regulated in Ilpum and down-regulated in NIL; 1,819 genes up-regulated in NIL and down-regulated in Ilpum) were identified. Interestingly, these DEGs were found to be involved in key physiological processes, with interesting molecular functions, including plant defense against diverse biotic stresses, hormone signaling, and other developmental processes. Based on the quantile normalization of the Fragments Per Kilobase of transcript per Million mapped reads (FPKM) values followed by student’s t-test (p <0.05) we identified 3,283 DEGs in Ilpum (1,935 upregulated and 1,348 downregulated) and 2,599 DEGs in NIL (1,621 up-regulated and 978 down-regulated) with at least log2 (logarithm base 2) 2-fold change (Log2FC) in expression upon GRH infestation.
Conclusions: The current study has provided the first RNA-Seq dataset and comparative transcriptome profile of GRH responsive genes from Ilpum (GRH-susceptible rice cultivar) and a near isogenic line (NIL) carrying Grh1 gene introduced from Shingwang into Ilpum to investigate the possible transcriptional interaction with other defense related genes. In addition, RNA-Seq data and MapMan analysis revealed the activation of multiple regulatory pathways following GRH infestation. Furthermore, the observed differential transcriptome profile between Ilpum and NIL would suggest the existence of a possible interaction network between Grh1 and other defense related genes towards GRH resistance in rice.

sample_organism:
Oryza sativa
Oryza sativa Japonica Group

overall_design:
Rice leaf mRNA profiles of 21-day-old wild type (WT) and Near Isogenic Line (NIL) infested with green rice leafhopper.

Grant information:
Project No. PJ01579401
This work was supported by the BioGreen21 Agri-Tech Innovation Program.

first: Yongho

last: Kwon

first: Nkulu

last: Kabange


title: Locus specific epigenetic modalities of random allelic expression imbalance

city: Paris Cedex 05

first: Dina

last: Zielinski

address: 26 rue d'ulm

institute: Institut Curie

summary: Genes are generally thought to be expressed from both alleles. There are some exceptions, including Random monoallelic expression (RME), even though its extent is still somewhat debated. We assessed whether and how some autosomal genes that we previously identified as being RME are prone to persistent and stable monoallelic expression. Not only do we confirm the occurrence of RME at large frequencies, our results also reveal unforeseen modes of allelic expression,that appear to be gene specific and epigenetically regulated. This non-canonical allelic regulation has large physiological and pathological implications and represents novel therapeutic perspectives.

overall_design: Male or female hybrid (129sv x Castaneus) mouse ES cells were differentiated into NPCs, as previously described (PMID 16086633, 24576422). NPC clones were generated following manual colony picking after limited dilution of the NPC population. Clones were individually expanded and then harvested for RNA extraction. NPC clones were differentiated into astrocytes as previously described (PMID 24576422).

first: Lucile

last: Poll

first: Benjamin

last: Foret

first: Florian

last: Massip

first: Mikael

last: Attia

first: Ava

last: Carter

first: Laurene

last: Syx

first: Howard

last: Chang

first: Anne-Valerie

last: Gendrel

first: Edith

last: Heard


title: Differential expression of Organ Transplant rejection related genes in Cp40 treated nonhuman primates

city: Durham

first: Jean

last: Kwun

state: NC

address: 207 Research Dr, Jones 362

department: Surgery

institute: Duke University

summary: Animals responded to Cp40 treatment (Late Rejector) showed a distinct pattern of gene expression compared to animals who did not respond (Early Rejector).

overall_design: In the study presented here, renal allografts from  Cp-40 (C3 inhibitor) treated highly sensitized NHP recipitnes were used to acquire expression profiles of a total of 758 genes using nanostring - nCounter Human Organ Transplant panel


title: Identification of response signatures for tankyrase inhibitor treatment in tumor cell lines

city: Oslo

first: Martin

middle: Frank

last: Strand

address: Prinsensgate 7

institute: Høyskolen Kristiania

summary:
Anti-cancer treatment, using small-molecule tankyrase 1 and tankyrase 2 (TNKS1/2) inhibition (TNKSi) shows effect against selected tumor cell lines and in mouse models. Here, we characterize the responsiveness signatures and in depth mechanisms for the anti-proliferative effect of TNKSi. The TNKS1/2-specific inhibitor G007-LK was screened against 537 human tumor cell lines, and a panel of in particular TNKSi-sensitive tumor cell lines was identified.
Transcriptome, proteome and bioinformatic analyses classified the overall TNKSi-induced response signatures in the selected panel. Prediction of TNKSi-mediated inhibition of WNT/β-catenin, YAP and PI3K/AKT signaling was validated and correlated with lost expression of the key oncogene MYC and impaired cell growth. Moreover, we show that TNKSi, when attenuating YAP signaling, induces accumulation of TNKS1/2-containing β-catenin degradosomes functioning as central complexes interacting with YAP and AMOT proteins. The findings provide a contextual and mechanistic framework for TNKSi in cancer cell lines rationalizing further comprehensive preclinical and clinical evaluations.

overall_design: Two biological replicates of 5 different cancer cell lines were treated with DMSO (0.01%) control or G007-LK (1 µM),  24 hours before RNA extraction

first: Mygland

last: Line

middle: F

first: Shoshy

last: Brinch

first: Petter

last: Olsen

first: Aleksandra

last: Aizenshtadt

first: Kaja

last: Lund

first: Nina

last: Solberg

first: Max

last: Lycke

first: Tor

last: Thorvaldsen

first: Sandra

last: Espada

first: Dorna

last: Misaghian

first: Page

last: Christian

first: Oleg

last: Agafonov

first: Nygård

last: Ståle

first: Nai-Wen

last: Chi

first: Eva

last: Lin

first: Jenille

last: Tan

first: Yihong

last: Yu

first: Mike

last: Costa

first: Stefan

last: Krauss

first: Waaler

last: Jo


title: Early life antibiotics influence in vivo and in vitro mouse intestinal epithelium maturation and functioning

status: Public on Jun 01 2021

city: Amsterdam

first: Sander

last: Meisner

state: NH

address: Meibergdreef 69-71

department: Tytgat institute

institute: AMC

summary: Background & Aims  The use of antibiotics (AB) is a common practice during the first months of life. AB can perturb the intestinal microbiota, indirectly influencing the intestinal epithelial cells (IECs), but also directly affect IECs, independent of the microbiota.  Previous studies in rodents have mostly focused on the impact of AB treatment during adulthood. However, the difference between the adult and neonatal intestine warrants careful investigation of the effects of AB in early life.    Methods  Neonatal mice were treated with a combination of amoxicillin, vancomycin, and metronidazole, from postnatal day 10 to 20. Intestinal permeability and whole intestine gene and protein expression were analyzed. IECs were FACS-sorted and their genome-wide gene expression analyzed. Mouse fetal intestinal organoids were treated with the same AB combination and their gene and protein expression, and metabolic capacity determined.  Results  We found that in vivo treatment of neonatal mice led to decreased intestinal permeability and reduced number of specialized vacuolated cells, characteristic of the neonatal period and necessary for absorption and digestion of milk macromolecules. Additionally, the expression of genes typically present in the neonatal intestinal epithelium was lower, whereas the adult gene expression signature was higher. Moreover, we found altered epithelial defense and transepithelial sensing capacity. In vitro treatment of intestinal fetal organoids with AB showed that part of the consequences observed in vivo is a result of a direct action of the AB on IECs. Lastly, AB reduced the metabolic capacity of intestinal fetal organoids.      Conclusion  Our results demonstrate that early life AB treatment induces direct and indirect effects on IECs, influencing their maturation and functioning.

overall_design: Postnatal (P)10 C57BL/6 wild-type mice pups were randomly distributed in 2 groups: treatment group (2 litters, 6 pups per litter) and control group (2 litters, 6 pups per litter). Treatment group received daily via oral gavage antibiotic mix (25mg/kg/day amoxicillin, 50mg/kg/day metronidazole, and 50mg/kg/day vancomycin), while control group received PBS. At P20, proximal and distal small intestine were separated and epithelial cells were FACS-sorted using the EpCAM marker. The epithelial cells of 3 different pups, belonging to the same litter, were combined into one sample, resulting in 4 samples per group. RNA was extracted and microarray analysis was performed using Affymetrix Clariom® S 8-Array HT Plate

first: Tânia

last: Martins Garcia

first: Manon

last: van Roest

first: Wouter

middle: L

last: Smit

first: Jacqueline

last: Vermeulen

first: Joana

last: Silva

first: Pim

last: Koelink

first: Jan

last: Koster

first: William

last: Faller

last: Wildenberg

first: Ruurd

last: van Elburg

first: Vanesa

last: Muncan

first: Ingrid

last: Renes


title: Gene expression changes by telomere shortening in human colonic organoids

status: Public on Jun 24 2021

city: yushima bunnkyoku Tokyo

first: Sho

last: Watanabe

department: gastroenterology

institute: Tokyo medical and dental university

summary: Gene expression changes of UC-model organoids derive from human colon indcued by telomere enlongation was assessed by Madecassoside treatemt (telomerase activator). Gene expression changes of human colon organoids induced by telomere shortening was assessd by MST-312 treatment (telomerase inhibitor).

overall_design:
GSEA analysis was performed about RNA1-3 vs RNA4-6 and RNA7 vs RNA8.
MD-treated UC-model organoids vs UC-model organoids / control organoids vs MST-312 treated organoids

first: Kiichiro

last: Tsuchiya


title: RNA seq and MeRIP-seq of COV434 cells before and after FTO knockdown

status: Public on Jun 15 2021

first: Zhongxin

last: Jiang

address: No.515 Fengyang Road

department: Reproductive medical center，Changzheng Hospital

institute: Naval Medical university

summary: Multifunctional N6-methyladenosine (m6A) has been revealed to be an important epigenetic component in various physiological and pathological processes, but its role in female ovarian aging remains unclear. Thus, we demonstrated m6A demethylase FTO downregulation and the ensuing increased m6A in granulosa cells (GCs) of human aged ovaries, while FTO-knockdown GCs showed faster aging-related phenotypes mediated. Using the m6A-RNA-sequence technique (m6A-seq), increased m6A was found in the FOS-mRNA-3'UTR, which is suggested to be an erasing target of FTO that slows the degradation of FOS-mRNA to upregulate FOS expression in GCs, eventually resulting in GC-mediated ovarian aging. FTO acts as a senescence-retarding protein via m6A, and FOS knockdown significantly alleviates the aging of FTO-knockdown GCs.

overall_design: COV434 cells were transfected by negative control lentivirus(COV434-shNC) and Fto-knockdown lentivirus(COV434-shFTO) for 3 times. 6 simples were get by this way.  RNA seq was done with half of each simples and MeRIP-seq(FTO antibodies were used) was done with another half of each simples.

first: Wen

last: Li

first: Fu

last: Yang

first: Ningxia

last: Sun


title: Transcriptome Analysis of Dihydrotestosterone-treated 2D- and 3D-cultured Dermal Papilla Cells

city: Guangzhou

first: Yuxin

last: Chen

address: Nanfang Dadao Street, Baiyun district

summary: Hair follicle growth inhibitory effect of dihydrotestosterone (DHT)-treated two-dimensional (2D)- and 3D-cultured DPCs were evaluated. 2D- and 3D-cultured DPC proliferation was inhibited after co-culturing with outer root sheath (ORS) cells under DHT treatment. Moreover, gene expression levels of β‐catenin and neural cell adhesion molecule (NCAM) were significantly decreased and those of cleaved caspase-3 significantly increased in 2D- and 3D-cultured DPCs with increasing DHT concentrations. ORS cell proliferation also significantly increased after co-culturing in the control-3D model compared with the control-2D model. ki67 downregulation and cleaved caspase-3 upregulation in DHT-2D and 3D groups significantly inhibited ORS cell proliferation. Sequencing showed an increase in the expression of genes related to extracellular matrix synthesis in the 3D model group. Additionally, the top 10 hub genes were identified, and the expression of nine chemokine-related genes in DHT-treated DPCs was found significantly increased. We also identified the interactions between transcription factor (TF)–genes and microRNAs with hub genes and the TF–microRNA coregulatory network. Overall, the findings indicate that 3D-cultured DPCs are more representative of in vivo conditions than are 2D-cultured DPCs, and contribute to our understanding of the molecular mechanisms underlying androgen-induced alopecia.

overall_design: Human hair follicles were taken from the balding (frontal) area of male patients undergoing hair transplantation surgery. Ethical approval and informed consent were obtained preoperatively from Nanfang Hospital of Southern Medical University. Dermal papillae were isolated from the bulbs of hair follicles, plated in a cell culture flask (Corning Inc., Corning, NY), and cultured in Dulbecco's Modified Eagle Medium (DMEM; Gibco, Waltham, MA) supplemented with 1% (v/v) penicillin–streptomycin and 20% (v/v) fetal bovine serum (FBS; Gibco) at 37 °C and 5% CO2. Once the outgrowth reached 80% confluence, human DPCs were harvested by incubation with 0.25% (w/v) trypsin/EDTA (Gibco) and transferred to new culture dishes at a split ratio of 1:2. For 3D culture, DPCs were seeded in an ultra-low attachment 96-well plate (Corning Inc.) with DMEM supplemented with 1% (v/v) penicillin–streptomycin and 10% (v/v) FBS. Spheroids were formed for 1 d after seeding and were used in the following assays.

first: Yufan

last: Zhang


title: Integration of spatial and single cell transcriptomics localizes epithelial-immune cross-talk in kidney injury

city: Indianapolis

first: Michael

last: Eadon

state: IN

address: 950 W Walnut St

institute: Indiana University

summary: Single cell sequencing studies have characterized the transcriptomic signature of cell types within the kidney. However, the spatial distribution of acute kidney injury (AKI) is regional and affects cells heterogeneously. We first optimized coordination of spatial transcriptomics and single nuclear sequencing datasets, mapping 30 dominant cell types to a human nephrectomy. The predicted cell type spots corresponded with the underlying histopathology. To study the implications of AKI on transcript expression, we then characterized the spatial transcriptomic signature of two murine AKI models: ischemia reperfusion injury (IRI) and cecal ligation puncture (CLP). Localized regions of reduced overall expression were associated with injury pathways. Using single cell sequencing, we deconvoluted the signature of each spatial transcriptomic spot, identifying patterns of colocalization between immune and epithelial cells. Neutrophils infiltrated the renal medulla in the ischemia model. Atf3 was identified as a chemotactic factor in S3 proximal tubules. In the CLP model, infiltrating macrophages dominated the outer cortical signature and Mdk was identified as a corresponding chemotactic factor. The regional distribution of these immune cells was validated with multiplexed CO-Detection by inDEXing (CODEX) immunofluorescence. Spatial transcriptomic sequencing complements single cell sequencing by uncovering mechanisms driving immune cell infiltration and detection of relevant cell subpopulations.

overall_design: A single human reference nephrectomy (female aged 59 without histologic evidence of kidney disease) was acquired from the Biopsy Biobank Cohort of Indiana (BBCI). From age-matched 8-10 week old 129/ SvEv mice (Taconic Biosciences, Albany, New York), tissues were acquired from a sham mouse in which the abdomen was opened and sutured back and mice which underwent ischemia-reperfusion injury (IRI) or cecal ligation and puncture (CLP). In the IRI model both renal pedicles were exposed and clamped for 22 minutes through a midline incision then released. In the CLP model, the cecum was ligated and punctured with a 25 gauge needle. Kidneys were excised upon sacrifice 6 hours after each procedure and frozen in Optimal Cutting Temperature (OCT) compound. Slide preparation (CG000240_Demonstrated_Protocol_VisiumSpatialProtocols_TissuePreparationGuide_Rev_A, 10X Genomics),  imaging  (CG000241_VisiumImagingGuidelinesTN_Rev_A, 10X Genomics), mRNA extraction, library preparation, and sequencing (CG000239_VisiumSpatialGeneExpression_UserGuide_RevD, 10X Genomics) were conducted according to Visium Spatial Gene Expression protocols . Frozen transverse 10 µm sections from the human nephrectomy or each murine model were placed within the etched frames of the capture areas on the active surface of the Visium Spatial Slide. Tissue sections were fixed in methanol and stained with hematoxylin and eosin (H&E). Stained tissue sections were permeabilized for 12 minutes, and the cDNA libraries were prepared and sequenced on an Illumina NovaSeq 6000 with 28bp+120bp paired-end sequencing mode.

first: Eadon

last: Michael

first: Ricardo

last: Melo Ferreira

first: Ying-Hua

last: Cheng


title: Benchmarking AAV-Cre mouse models for RNA-seq

city: Glasgow

first: Ania

last: Wilczynska

address: Switchback Road

institute: Beatson Insistute for Cancer Research

summary: This study reports the baseline effects of systemic (i.v.) administration of AAV8-TBG-null and AAV8-TBG-Cre on the liver of male, wild-type C57Black6/J mice. We performed polyA RNAseq of whole liver lysates from mice 2, 4 and 7 days post AAV8-TBG-null or AAV8-TBG-Cre administration and compared their transcriptome with that of male mice of similar age that didn't receive any AAV8 (day 0). We report some changes in gene expression of genes related to circadian rythm and response to infection at certain timepoints. Our results demonstrate that AAV8-TBG vectors can have minimal effects on the murine liver transcriptome, something that needs to be considered and controlled when using this system for mouse experiments. Finally, we hope that this dataset will help other researchers to correctly interpret data obtained from mouse experimentation using AAV8-TBG vectors.

overall_design: Creation of a control data set for AAV-Cre mouse models at different timepoints post viral induction in C57Bl6/J mice

first: Christos

last: Kiourtis

first: Thomas

last: Bird


title: Comprehensive molecular characterization of pediatric radiation-induced high-grade glioma

status: Public on May 27 2021

city: Memphis

first: Quynh

last: Tran

state: TN

address: 262 Danny Thomas Place, C4029, Mail Stop 250

department: Pathology

institute: St. Jude Children's Research Hospital

type: Methylation profiling by genome tiling array

summary: Radiation-induced high-grade gliomas (RIGs) are an incurable late complication of cranial radiation therapy. We performed DNA methylation profiling, RNA-seq, and DNA sequencing on 32 RIG tumors and an in vitro drug screen in two RIG cell lines. We report that based on DNA methylation, RIGs cluster primarily with the pediatric receptor tyrosine kinase I high-grade glioma subtype. Common copy-number alterations include Chromosome (Ch.) 1p loss/1q gain, and Ch. 13q and Ch. 14q loss; focal alterations include PDGFRA and CDK4 gain and CDKN2A and BCOR loss. Transcriptomically, RIGs comprise a stem-like subgroup with lesser mutation burden and Ch. 1p loss and a pro-inflammatory subgroup with greater mutation burden and depleted DNA repair gene expression. Chromothripsis in several RIG samples is associated with extrachromosomal circular DNA-mediated amplification of PDGFRA and CDK4. Drug screening suggests microtubule inhibitors/stabilizers, DNA-damaging agents, MEK inhibition, and, in the inflammatory subgroup, proteasome inhibitors as potentially effective therapies.

overall_design: Radiation-induced high-grade gliomas (RIGs) are an incurable late complication of cranial radiation therapy. We performed DNA methylation profiling on 32 RIG tumors.

first: John

last: Lucas

first: Brent

last: Orr

first: Tong

last: Lin


title: Genome-wide mapping of ASCL2 and CTNNB1 in hepatoblastoma cell lines

city: Meguro-ku

first: Genta

last: Nagae

state: Tokyo

address: 4-6-1, Komaba

department: Genome Science Division

institute: RCAST, University of Tokyo

summary: Hepatoblastoma (HB) is the most common pediatric liver malignancy; however, hereditary predisposition and acquired molecular aberrations related to HB clinicopathological diversity are not well understood. We performed an integrative genomic profiling of 163 pediatric liver tumors (154 HB and 9 hepatocellular carcinoma) based on data acquired from a cohort study (JPLT-2). The total number of somatic mutations was found to be extremely low (0.52 /Mb on exonic regions) but correlated with age at diagnosis. TERT promoter mutations are prevalent in the tween HBs, selective in the transitional liver cell tumor (TLCT, > 8 years old). DNA methylation profiling revealed that classical HBs are characterized by the specific hypomethylated enhancers, which are enriched with binding sites for ASCL2, a regulatory transcription factor for definitive endoderm in Wnt-pathway. Prolonged upregulation of ASCL2, as well as fetal-liver-like methylation patterns of IGF2 promoters, suggests their “cell of origin” derived from the premature hepatoblast, similar to intestinal epithelial cells, which are highly proliferative. Systematic molecular profiling of HB is a promising approach to understanding the epigenetic drivers of hepatoblast carcinogenesis and clues for risk stratification.

first: Aya

last: Nonaka

first: Akimasa

last: Hayashi

first: Takanori

last: Fujita

first: Hiroyuki

last: Aburatani


title: Adult Drosophila ovary single cell RNA sequencing

status: Public on May 31 2021

first: Maija

last: Slaidina

address: 540 1st ave

department: Skirball Institute

institute: New York University School of Medicine

summary: We have sequenced anterior part of the adult Drosophila ovary. The sample includes cells from the stem cell compartment (germarium) and up to stage 9 follicles.

overall_design: Ovaries were dissected from live animals, and cells were sequenced using the 10x Genomics Chrmomium system. More information in Slaidina, Guptas, Lehmann et al. 2021

first: Ruth

last: Lehmann


title: Single-cell transcriptome analysis of endothelial cell heterogeneity under laminar shear stress

status: Public on May 25 2021

city: WAUWATOSA

first: ZIQING

last: LIU

state: WI

address: 8701 W Watertown Plank Rd, BSB 5320

department: Biology

institute: Medical College of Wisconsin

summary: Heterogeneity of endothelial cells that form the innermost layer of all vessels is critical for vascular sprouting and angiogenesis. After new vessels form, endothelial cell heterogeneity is believed to be gradually lost as vessels respond to flow-mediated signals, mature, remodel and become homeostatic. However, whether and at what level endothelial cell lost heterogeneity is poorly understood. Here we investigated heterogeneity change of endothelial cells under homeostatic laminar shear tress in comparison to static cultures.

overall_design: We performed single-cell RNA sequencing of human umbilical vein endothelial cells (HUVEC) cultured under static condition or flowed under 15 dynes/cm2 laminar shear (Ibidi µ-Slide I Luer) for 72 hrs. Static and Flow samples were collected from two independent experiments (replicates) and sequenced using the 10x Genomics platform. To check doublet rate, 10% MEF were mixed with each sample of HUVEC right before loading onto 10X Genomics Chromium Controller for droplet generation.

first: Ziqing

last: Liu

first: Dana

last: Ruter

first: Victoria

last: Bautch


title: Macrophage deletion of Noc4l triggers endosomal TLR4/TRIF signal and leads to insulin resistance

status: Public on May 22 2021

city: Beijing

first: Yongli

last: Qin

address: Yuanmingyuan Road 2

institute: China agricultural university

summary: To study the role of noc4l in macrophages in inflammation induced insulin resistance, BMDM cells were isolated from Noc4l wild type or Noc4l knock out mouse and then treated with or without LPS.  By using microarray expression profiling with RNA extrated from BMDMs, we found Noc4l was related to inflammation.

overall_design: BMDM cells were isolated from Noc4l wild type or Noc4l knock out mice and treated with or without 100ng/ml LPS for 16h. Total RNAs of BMDMs were isolated and purified,  and hybridized to the SurePrint G3 Mouse GE 8x60K microarray (Agilent). Microarray slides were washed and scanned with a DNA Microarray Scanner (Agilent), according to the standard protocol of the manufacturer.

first: Lina

last: Jia

first: Xiangdong

last: Li


title: Changes in gene expression when expressing two sets of t(6;11) fusion proteins

city: Frankfurt am Main

first: Lukas

last: Jost

address: Altenhöferallee 3

institute: GenXPro GmbH

summary: We have cloned two sets of t(6;11) fusion genes with breakpoints in the majorand minor BCR of the MLL/KMT2A gene. Both setsof fusion genes were stably transfected alone or in combiantion to analyze their molecular power

overall_design: Fusion genes were constructed by fusing distinct cDNA portions of MLL/KMT2A with AF6/AFDN via a short intronic sequence

first: Rolf

last: Marschalek


title: Adipocytes disrupt the translational programme of Acute Lymphoblastic Leukaemia to favour tumour survival and persistence [Nalm-6]

city: London

first: Quentin

last: Heydt

address: Charterhouse Square

institute: Barts Cancer Institute

summary: Reprogramming of bone marrow microenvironments (BMMs) is a key process by which ALL cells gain resilience however the specific adaptations that facilitate primary disease and ALL survival after induction chemotherapy remain unclear. Using temporal analysis of clinical biopsies we identify that BM adipocytes are profoundly remodelled during ALL pathogenesis and treatment transitioning from cellular depletion within the primary leukaemia niche to a fully restored state upon remission treatment highlighting the specific and selective participation of adipocyte stroma in the chemotherapy context.  The functional relevance of these dynamics was revealed through modelling studies demonstrating that adipocytes non- cell autonomously regulate ALL development by reducing proliferative capacity whilst simultaneously increasing leukaemia cell quiescence. Thus, adipocyte dynamics mark a transition in the functional organisation of BMM from one that favours emergent ALL to an adverse setting for chemotherapeutic effects. Mechanistically, we show that adipocyte induced tumour suppression, accompanies rapid but reversible non canonical translational arrest revealing a novel regulatory relationship that executes at the level of the leukaemia proteome to lower ALL expansion. Importantly, adipocyte remodelled ALL proteomes adopt a distinct, reversible, stress-resistant state which was independent of cell cycle status underscoring the importance of therapy emergent adipocyte niches in conferring global tumour cell protection. These studies reveal the critical contribution of adipocyte mediated repression of the ALL proteome as another mode of microenviromental intervention advantaging ALL tumours to prevent their elimination.

overall_design: RNA-seq experiment with n=3 biological replicates of Nalm-6 co-cultured with 3T3-L1 Pre-adipocytes or 3T3-L1 Adipocytes as described

first: Chrysi

last: Xintaropoulou

first: Bela

last: Patel


title: Adipocytes disrupt the translational programme of Acute Lymphoblastic Leukaemia to favour tumour survival and persistence [BM-MSC]

overall_design: RNA-seq experiment with n=3 biological replicates of Healthy MSCs and ALL MSCs as described


title: Adipocytes disrupt the translational programme of Acute Lymphoblastic Leukaemia to favour tumour survival and persistence

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Unraveling the functional role of DNA demethylation at specific promoters by targeted steric blockage of DNA methyltansferase with CRISPR/dCas9 (ChIP-Seq)

status: Public on May 12 2021

city: Montreal

first: Moshe

last: Szyf

state: QC Quebec

address: 3655 Promenade Sir William Osler, Room 1309

department: Pharmacology & Therapeutics

country: Canada

institute: McGill University

summary: Although associations between DNA methylation and gene expression were established four decades ago, the causal role of DNA methylation in gene expression remains unresolved. Different strategies to address this question were developed; however, all are prone to confounds and may fail to disentangle cause and effect. We developed here a highly effective new method using only deltaCas9(dCas9):gRNA site-specific targeting to physically block DNA methylation at specific targets in the absence of a confounding flexibly-tethered enzymatic activity, enabling examination of the role of DNA demethylation per se in living cells. We show that the extensive induction of gene expression achieved by TET/dCas9-based targeting vectors is confounded by DNA methylation-independent activities, inflating the role of DNA methylation in the promoter region. Using this new method, we show that in several inducible promoters, the main effect of DNA methylation is silencing basal promoter activity. We find no credible evidence of off-target DNA demethylation as a consequence of gRNA binding. Thus, the effect of demethylation of the promoter region in these genes is small, while induction of gene expression by different inducers is large and DNA methylation independent. In contrast, targeting demethylation to the pathologically silenced FMR1 gene targets robust induction of gene expression. We also found that standard CRISPR/Cas9 knockout generates a broad unmethylated region around the deletion, which might confound interpretation of CRISPR/Cas9 gene depletion studies. In summary, this new method could be used to reveal the true extent, nature, and diverse contribution to gene regulation of DNA methylation at different regions.

overall_design: Anti-FLAG ChIP-sequencing of NIH-3T3 cells in triplicates in order to determine off-target binding sites of dCas9(3XFLAG) with either scrambled non-targeting guideRNA (gRNAscr) or a guideRNA targeting the transcription start site of the shorter isoform of IL33 (gRNA3).

first: Daniel

last: Sapozhnikov


title: A comprehensive map of alternative polyadenylation in African American and European American lung cancer patients

status: Public on May 13 2021

city: Bethesda

first: Josh

last: Stone

state: MD

address: 9000 Rockville Pike

department: CCR

institute: National Cancer Institue

summary:
We report the application of a novel method and analysis pipeline that sequences 3’end -enriched RNA to comprehensively map the APA landscape in lung cancer.
The goals of this study are to identify the functional role of APA in determining transcriptomic heterogeneity in lung cancer and  population differences in APA.

overall_design:
Ninety-eight patients with histologically confirmed non-small cell lung cancer were selected from the National Cancer Institute-Maryland (NCI-MD) lung cancer study. The study includes 98 human tumor tissues and 98 adjacent non-involved tissues (n=196 total).
AA = African American
EA = European American

first: Brid

last: Ryan

first: Adriana

last: Zingone


title: Molecular characterization of quiescent melanoma cells

status: Public on May 18 2021

city: Callaghan

first: Ting

last: La

state: NSW

address: University Drive

institute: UON

summary: Cancer dormancy is closely associated with cellular quiescence, a state whereby cells exit the cell cycle and are reversibly arrested in G0 phase. Curative cancer treatment thus requires therapies that either sustain the dormant state of quiescent cancer cells, or preferentially, eliminate them. However, the mechanisms responsible for the quiescent survival of these cells remain obscure. We took advantage that quiescent cells characteristically negative for the proliferation marker Ki67 and express high levels of the cyclin-dependent kinase (CDK) inhibitor p27 to develop a CRISPR/Cas9-based system to fuse a green fluorescent protein (EGFP) gene with endogenous CDKN1B, the gene encoding p27, and a red fluorescent protein (mCherry) gene with endogenous MKI67, the gene encoding Ki67 in the genome of human melanoma cells.  Flow cytometry were used to  isolate the viable quiescent (p27high/Ki67low) cells. The isolated quiescent and cycling cancer cells were subjected to RNA-seq

overall_design: By use of CRISPR-Cas9 genome editing, we introduced sequences encoding EGFP at the locus of CDKN1B, the gene encoding p27, and sequences encoding mCherry at the locus of MKI67, the gene encoding Ki67, into Mel-RM melanoma cells. The cycling (C, EGFP-p27lowmCherry-Ki67high cells ) and quiescent (Q, EGFP-p27highmCherry-Ki67low cells ) populations were isolated from this dually edited cells and subjected to RNA sequencing.

first: Xu

middle: D

last: Zhang

first: Lei

last: Jin


title: SarA regulon in S. aureus

status: Public on May 11 2021

city: Hanover

first: Liviu

last: Cengher

address: 45 Dewey Field Rd

department: Microbiology and Immunology

institute: Geisel School of Medicine


title: New genomic resources and comparative analyses reveal differences in floral gene expression in selfing and outcrossing Collinsia sister species

city: Philadelphia

first: Lauren

middle: Jeane

last: Frazee

state: PA

institute: Temple University

summary: We used flower bud transcriptomes from Collinsia rattanii and its predominantly outcrossing sister species, C. linearis, to explore the genomic basis of mating system and phenotypic evolution in Collinsia, a self-compatible genus. Transcriptional regulation of enzymes involved in pollen formation may influence floral traits that distinguish selfing and outcrossing Collinsia species through pleiotropic functions. These patterns provide clues about parallel evolution in selfing plants.

overall_design: We sampled 2-4 whole floral buds (= 1 sample) per bud stage from each of 3 individuals per species.

first: Joanna

last: Rifkin

first: Dinusha

middle: C

last: Maheepala

first: Alannie-Grace

last: Grant

first: Stephen

last: Wright

first: Susan

last: Kalisz

first: Amy

last: Litt

first: Rachel

last: Spigler


title: SarA regulon in S. aureus (RNA-seq)

summary: We have studied the transcriptome of S. aureus HG003 strain and HG003 DsarA strain

overall_design: 2 points growth, 2 strains, RNA extraction of WT and DsarA HG003 strains

first: Oriol

last: Charlotte

first: Cengher

last: Liviu

first: Manna

last: Adhar

first: Mauro

last: Tony

first: Pinel-Marie

last: Marie-Laure

first: Rouillon

last: Astrid

first: Cheung

last: Ambrose

first: Felden

last: Brice


title: Effects of Exportin5 (Exp5) knockdown on microRNA (miRNA) expression in human 293T cells

status: Public on May 08 2021

city: Nanjing

first: Yan

last: Zeng

state: Jiangsu

address: XuanWu District, No.1 WeiGang

institute: Nanjing Agricultural University

summary: Exp5 is a nuclear export factor in the animal miRNA biogenesis pathway.  This experiment examined how reduced Exp5 levels affected miRNA expression profiles.

overall_design: Human 293T cells were transiently transfected with a control or Exp5 small interfering RNA (siRNA).  Five days later total RNA was isolated and subjected to custom miRNA microarray analysis.


title: SarA regulon in S. aureus (ChIP-seq)

first: Liviu

last: Cengher

summary: ChIP seq for SarA in S. aureus HG003 wild type and HG003 DsarA

overall_design: Chromatin immunoprecipitation of DNA binding protein SarA-myc and associated cross-linked DNA in Wildtype and DsarA HG003


title: Transcriptome profile of S. cerevisiae strains expressing mistranslating tRNAs

first: Matthew

last: Berg

state: Ontario

address: 1151 Richmond St

department: Biochemistry

institute: University of Western Ontario

summary: Mistranslation, the mis-incorporation of an amino acid not specified by the “standard” genetic code, occurs in all cells. tRNA variants that increase mistranslation arise spontaneously and engineered tRNAs can achieve mistranslation frequencies approaching 10% in yeast and bacteria. The goal of this study was to assess the transcriptome changes in yeast cells expressing two different mistranslating tRNA variants which mistranslate at similar frequencies (of ~ 3%) but result in different substitutions, namely alanine at proline codons or serine at arginine codons.

overall_design: RNA sequencing of yeast strains expressing tRNA-Pro(G3:U70) or tRNA-Ser(UCU, G26A) compared to a wild-type yeast strain expressing no mistranslating tRNA

first: Christopher

middle: J

last: Brandl


title: Differentially expressed genes  in HNSCC tissues, normal oral epithelial tissues and CAFs

status: Public on May 01 2021

city: chiba

first: sachi

last: oshima

state: chiba

address: 1-8-1 inohana chuo-ku

department: Grad. Sch. Med

institute: Chiba Univ

summary: To identify differentially expressed genes by HNSCC tissues, normal oral epithelial tissues and CAFs were subjected to Agilent whole genome microarrays.

overall_design: All specimens and CAFs used in the study were obtained by surgical resection at Chiba University Hospital.

first: Naohiko

last: Seki

first: Sachi

last: Oshima


title: Tbet vs Eomes [RNA-Seq]

status: Public on May 10 2021

city: Lyon

first: Thierry

last: Walzer

address: 21 avenue tony garnier

institute: CIRI, centre international de recherche en infectiologie

summary: T-bet and Eomes are related T-box transcription factors that control NK cell development. This study was designed to understand the specific roles of Eomes and T-bet in regulating gene expression. RNAseq data were generated for immature (CD11b- CD27+) and mature (CD11b+ CD27-) NK cells from T-bet KO (Tbet Ho) or control mice (Tbet WT) or from Eomes KO (Eomes Ho) or control mice (NK-Cre). Three samples were generated for each condition (Tri 1, 2, 3).

overall_design: Three biological replicates for each condition were performed (ie three different flow cytometry sorts for each genotype and for each maturation stage).


title: Tbet-Eomes


title: Structural recognition of the mRNA 3’ UTR by PUF-8 restricts the lifespan of C. elegans

city: Hefei

first: Zheng

last: Xu

state: Anhui

address: Huangshan road

department: Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine

institute: University of Science and Technology of China

summary: The molecular mechanisms of aging are unsolved and fascinating fundamental biological questions. Caenorhabditis elegans is an ideal model organism for investigating aging. PUF-8, a PUF (Pumilio and FBF) protein in C. elegans, is crucial for germline development through binding to the 3’ untranslated regions (3’ UTR) in the mRNA of target genes. Recently, PUF-8 was reported to alter mitochondrial dynamics and mitophagy by regulating MFF, a mitochondrial fission factor, and subsequently regulate longevity. Here, we determined the crystal structure of the PUF domain of PUF-8 with an RNA substrate. Mutagenesis experiments were performed to alter PUF-8 recognition of its target mRNAs. We generate these mutations in C. elegans, those mutations reduced the fertility and extended the lifespan. We deep sequenced total mRNAs from wild-type and puf-8 mutant worms and conducted in vitro RNA pull-down experiments. Six PUF-8 regulated genes were identified, in which their mRNA 3’ UTRs contain at least one PUF-binding element (PBE). One of the six genes, pqm-1, is crucial for lipid storage and aging process. Knockdown of pqm-1 could revert the lifespan extension of puf-8(-) animals. Therefore, PUF-8 may regulate the lifespan of C. elegans via modulating pqm-1-related pathways

overall_design: In this study, we compared total mRNAs from (1) control animals; (2) puf-8(ust221) mutant; (3) puf-8(ust222) mutant; (4) puf-8(ust223) mutant; (5) puf-8(ok302).


title: The combined action of Esrrb and Nr5a2 is essential for naïve pluripotency.

status: Public on May 04 2021

city: paris

first: Pablo

last: Navarro

address: 25 rue du Docteur Roux

institute: Institut Pasteur

summary: The maintenance of pluripotency in mouse embryonic stem cells (ESCs) is governed by the action of an interconnected network of transcription factors. Among them, only Oct4 and Sox2 have been shown to be strictly required for the self-renewal of ESCs and pluripotency, particularly in culture conditions where differentiation cues are chemically inhibited. Here, we report that the conjunct activity of two orphan nuclear receptors, Esrrb and Nr5a2, parallels the importance of that of Oct4 and Sox2 in naïve ESCs. By occupying a large common set of regulatory elements, these two factors control the binding of Oct4, Sox2 and Nanog to DNA. Consequently, in their absence the pluripotency network collapses and the transcriptome is substantially deregulated, leading to the differentiation of ESCs. Altogether, this work identifies orphan nuclear receptors, previously thought to be performing supportive functions, as a new set of core regulators of naïve pluripotency.

overall_design: RNA-seq in mouse ES cells grown in FCS/LIF or 2i/LIF comparing the depletion of Esrrb, Nr5a2, or both factors to control. ChIP-seq of Esrrb and Nr5a2 in mouse ES cells grown in FCS/LIF. ChIP-seq of Esrrb, Oct4, Sox2, Nanog in 2i/LIF in control and the after individual or combined loss of Esrrb and Nr5a2.

first: Nicola

last: Festuccia

first: Nick

last: Owens


title: Transcriptome sequencing of Verticillium dahliae and △VdBre1 mutant

status: Public on May 20 2021

first: Huan

last: Wang

state: Beijing

address: NO.1 Beichen West Road

institute: institute of microbiology

summary: The soil-borne ascomycete Verticillium dahliae which causes wilt disease in many important crops results a severe reduction in crop yield and quality. During infection, the V.dahliae will secrete a lot of secondary metabolites which act as toxic factors to promote the infection process. However, the mechanism underlying how V.dahliae secondary metabolites regulate cotton infection remains largely unexplored. BRE1 is a highly conserved ubiquitin ligase (E3) enzymes and regulate expression of specific genes related to the production of secondary metabolites. To get an insight into the genes regulated by VdBre1, the comparative transcriptomic analysis was conducted between VdBre1 deletion mutant and the wild type V592. The conidia of wilde type and mutant were collected and total RNA was extracted using fungal RNA kit, sequencing was performed on an BGISEQ-500 platform.

overall_design: Conidia mRNA profiles of V. dahliae and △VdBre1 mutant were generated by sequencing, using BGISEQ-500 platform


title: Comparitive transcriptome analysis of two zebrafish mutants goosepimples/myovb and romeharsha

city: Mumbai

first: Mahendra

last: Sonawane

state: Maharashtra

address: Homi bhabha road, navy nagar

department: Biological Sciences

country: India

institute: Tata Institute of Fundamental Research

summary: This dataset comprises RNA-Seq data from two zebrafish mutants and their respective sibling controls. These mutants show trafficking defects leading to accumuation of early and late endocytic vesicles and rounding up in the periderm. The goosepimples mutation has been identified as a null form of MyoVb, an actin based motor. Differential expression analysis suggests upregulation of grainyhead familiy transcription factors Grhl1 and Grhl3 along with various adhesion associated genes.

overall_design: RNA was extracted from 20 representative mutant and sibling embryos out of three clutches per mutant (goosepimples siblings, goosepimples mutants, romeharsha siblings, romeharsha mutants) at 48 hours post fertilization cDNA was prepared and sequencing was performed on Illumina Hi seq 2000

first: Mandar

last: Phatak

middle: S


title: Blastic plasmacytoid dendritic cell neoplasm: genomics mark epigenetic dysregulation as a primary therapeutic target

status: Public on May 03 2021

city: New York

first: Raul

last: Rabadan

state: NY

institute: Columbia University

summary: Blastic plasmacytoid dendritic cell neoplasm (BPDCN) is a rare and aggressive hematologic malignancy for which there is still no effective therapy. In order to identify genetic alterations useful for a new treatment design, we used whole-exome sequencing to analyze 14 BPDCN patients and the patient-derived CAL-1 cell line. The functional enrichment analysis of mutational data reported the epigenetic regulatory program to be the most significantly undermined (P<0.0001). In particular, twenty-five epigenetic modifiers were found mutated (e.g. ASXL1, TET2, SUZ12, ARID1A, PHF2, CHD8); ASXL1 was the most frequently affected (28.6% of cases). To evaluate the impact of the identified epigenetic mutations at the gene-expression and Histone H3 lysine 27 trimethylation/acetylation levels, we performed additional RNA and pathology tissue-chromatin immunoprecipitation sequencing experiments. The patients displayed enrichment in gene signatures regulated by methylation and modifiable by decitabine administration, shared common H3K27-acetylated regions, and had a set of cell-cycle genes aberrantly up-regulated and marked by promoter acetylation. Collectively, the integration of sequencing data showed the potential of a therapy based on epigenetic agents. Through the adoption of a preclinical BPDCN mouse model, established by CAL-1 cell line xenografting, we demonstrated the efficacy of the combination of the epigenetic drugs 5’-azacytidine and decitabine in controlling disease progression in vivo.

overall_design: Molecular characterization of BPDCN cases by Whole-Exome and RNA sequencing.

first: Maria

middle: R

last: Sapienza

first: Francesco

last: Abate

first: Claudio

last: Tripodo

first: Stefano

middle: A

last: Pileri


title: Extracellular Succinate Hyperpolarizes M2 Macrophages through SUCNR1/GPR91-Mediated Gq Signaling

status: Public on Apr 30 2021

city: Oxford

first: Chris

last: O'Callaghan

state: Oxfordshire

address: Roosevelt Drive

department: Nuffield Department of Medicine

institute: University of Oxford

summary: Succinate functions both as a classical TCA cycle metabolite and as an extracellular metabolic stress signal sensed by the mainly Gi-coupled succinate receptor, SUCNR1. In the present study, we characterize and compare effects and signaling pathways activated by succinate and both classes of non-metabolite SUCNR1 agonists. By use of specific receptor and pathway inhibitors, rescue in G protein depleted cells and monitoring of receptor G protein activation by BRET we surprisingly identify Gq rather than Gi signaling, to be responsible for SUCNR1-mediated effects on basic transcriptional regulation. Importantly, in primary human M2 macrophages, where SUCNR1 is highly expressed, we demonstrate that physiological concentrations of extracellular succinate act through SUCNR1 activated Gq signaling to efficiently regulate transcription of immune function genes in a manner that hyperpolarizes their M2 versus M1 phenotype. Thus, sensing of stress-induced extracellular succinate by SUCNR1 is an important transcriptional regulator in human M2 macrophages through Gq signaling.

overall_design: RNA-seq of primary human monocyte-derived macrophages from healthy adult donors. Macrophages were polarised to the M2 state and treated with succinate +/- a SUCNR1 antagonist or a Gq inhibitor and compared with a vehicle control.

first: Thomas

last: Hiron

first: Da

last: Lin


title: Leveraging histone modifications to improve genome annotation

status: Public on Apr 26 2021

city: Athens

first: Robert

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

summary: With the creation of accurate, chromosome-scale genomes, the next challenge facing the genomics community is the accurate idenfication of transcriptional units, distinguishing them from aberrant transcriptional noise. This has proven to be a challenge as annotation by traditional means, such as short read RNA-seq followed by transcriptome assembly, which is prone to the generation of in-silico artifacts. To address this issue, we took advantage of epigenomic data in the form of ChIP-seq to unbiasedly annotate plant genomes and identify potential annotation issues, as well as identify novel genes. Histone modifications appear in the genome in a reproducible and predictable manner, making them an ideal resource to use in annotation. Trimethylation of histone 3 lysine 4 (H3K4me3), as well as acetylation of  histone 3 lysine 56 are well documented to coincide with initiation of transcription by polymerase II (Pol II) at promoter sequences. These initiation marks, paired with marks deposited across the gene body during transcriptional elongation, such as histone 3 lysine 36 tri-methylation (H3K36me3) and histone 3 lysine 4 mono-methylation (H3K4me1), offer a framework to begin identifying complete transcriptional units. We leveraged these data on a genome-wide scale, allowing for identification of annotations discordant with empirical data. In total, 13,159 potential annotation issues were found in Zea mays across three different tissues, which were corroborated using complementary RNA-based approaches. Upon correction and validation, genes were extended by an average of 2,128 base pairs, and the length of discovered novel genes was 1,962 base pairs. Application of this method to five additional plant genomes revealed a variety of novel gene annotations, including 13,836 in Asparagus officianalis, 2,724 in Setaria viridis, 2,446 in Sorghum bicolor, 8,631 in Glycine max, and 2,585 in Phaseolous vulgaris.

sample_organism:
Glycine max
Zea mays

platform_organism:
Glycine max
Zea mays

overall_design: ChIP-seq of histone modification H3K36me3, H3K4me1, and H3K56ac for Glycine max.  ChIP-seq for H3K4me1 of Zea mays ear

last: Medieta

first: Xuan

last: Zhang